Abstract
<title>Abstract</title> <p> Urbanisation represents one of the most powerful contemporary drivers of evolution. Yet, the genomic basis of adaptation to urban environments remains understudied, particularly in highly mobile vertebrates. We investigated population structure and genomic signatures of selection in common kestrels ( <italic>Falco tinnunculus</italic> ) in urban and non-urban environments. Using whole-genome sequencing data, we found limited genome-wide differentiation and high connectivity among habitats, indicating substantial gene flow. Nonetheless, composite selection scans revealed distinct habitat-specific genomic regions under selection. In urban kestrels, a strong signal on chromosome 1 included <italic>ANKRD50</italic> , a gene associated with viral response, suggesting pathogen-mediated selection in urban habitats, and RELN gene, associated with neuronal functions. Non-urban kestrels showed selection on genes involved in lipid metabolism ( <italic>CDS1</italic> , <italic>PIK3CB</italic> ), neuronal functions ( <italic>NAPEPLD</italic> , <italic>RELN</italic> ), DNA damage response ( <italic>BOD1L1</italic> ), circadian rhythm ( <italic>PER2</italic> ), and growth regulation ( <italic>FAM155A</italic> ). These results indicate that adaptive divergence can occur at specific loci despite extensive connectivity. Further studies involving other study areas will be important to assess the generality of our findings. </p>